In atmospheric transport models, the covariation of the atmospheric transport and annually neutral biospheric CO2 flux is usually evident as the annual zonal mean surface CO2 concentration gradient. Using the NIES transport model and CO2 flux from the Biome-BGC model, the covariations of different transport mechanisms and CO2 flux were examined and quantified. Including the covariation of the total transport (processes included in the NIES model) and CO2 flux, the annual average pole to pole CO2 concentration gradient is 3.5 ppm and interhemispheric difference of the average extratropical surface concentration is 2.5 ppm. The conventional covariation mechanism of the seasonal variation of planetary boundary layer mixing height and CO2 flux accounts for approximately 45% of the CO2 concentration gradient. Another important contribution to the CO2 concentration gradient in this model is the covariation of the extratropical anomaly transport (mainly by cyclones and anticyclones) and the biospheric flux, which accounts for about 55%. This alternate physical mechanism is the association of stronger meridional (north–south) anomaly transport (under strong baroclinic instability condition) with higher CO2 concentration from soil respiration in the winter and weaker anomaly transport (weak baroclinic instability condition) with lower CO2 concentration from photosynthetic uptake in the summer. The net result of the meridional transport and flux covariation is a north–south annual zonal mean CO2 concentration gradient.